Liam-Research-2-Integration

library(tidyverse)
library(tuneR)
library(devtools)
library(ggplot2)
library(tsfeatures)
library(class)
library(cvTools)
library(randomForest)
library(GEOquery) 
library(R.utils)
library(reshape2)
library(limma)
library(dplyr)
library(e1071)
library(DT)
library(viridis)
library(plotly)
library(scales)

gse36059 = getGEO("GSE36059")[[1]]

Found 1 file(s)
GSE36059_series_matrix.txt.gz
Using locally cached version: C:\Users\lmcca\AppData\Local\Temp\RtmpC6OZAY/GSE36059_series_matrix.txt.gz
Warning in for (getMethodName in getMethodNames) { :
  closing unused connection 5 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36059/matrix/)
Warning in .Internal(lapply(X, FUN)) :
  closing unused connection 4 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36059/matrix/)
Warning in .Internal(lapply(X, FUN)) :
  closing unused connection 3 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48581/matrix/)
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpC6OZAY/GPL570.soft.gz 

gse48581 = getGEO("GSE48581")[[1]]

Found 1 file(s)
GSE48581_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpC6OZAY/GPL570.soft.gz 

gse129166 = getGEO("GSE129166")[[1]]

Found 1 file(s)
GSE129166_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpC6OZAY/GPL570.soft.gz 

gse36059_f = fData(gse36059)
gse36059_f

gse48581_f = fData(gse48581)
gse48581_f

gse129166_f = fData(gse129166)
gse129166_f

gse36059_p = pData(gse36059)
gse36059_p

gse48581_p = pData(gse48581)
gse48581_p

gse129166_p = pData(gse129166)
gse129166_p

#Remove Nephrectomy outcomes
gse36059_p = gse36059_p[!(gse36059_p$characteristics_ch1=="diagnosis: Nephrectomy"),]

gse48581_p = gse48581_p[!(gse48581_p$characteristics_ch1=="diagnosis (tcmr, abmr, mixed, non-rejecting, nephrectomy): nephrectomy"),]

#Encodes stable as 0 and rejecting as 1
gse36059_p$diagnosis = ifelse(gse36059_p$characteristics_ch1 == "diagnosis: non-rejecting", 0, 1)
gse48581_p$diagnosis = ifelse(gse48581_p$characteristics_ch1.1 == "diagnosis (tcmr, abmr, mixed, non-rejecting, nephrectomy): non-rejecting", 0, 1)
gse129166_p$diagnosis = ifelse((gse129166_p$characteristics_ch1.1 == "tcmr (no: 0_borderline:1_TCMR:2): 0") & (gse129166_p$characteristics_ch1.2 == "abmr (no: 0_Yes:1): 0"), 0, 1)

#Encodes stable as 0, ABMR as 1, TCMR as 2, Mixed as 3
gse36059_p$exact_diagnosis = ifelse(gse36059_p$characteristics_ch1 == "diagnosis: non-rejecting", 0, ifelse(gse36059_p$characteristics_ch1 =="diagnosis: ABMR", 1, ifelse(gse36059_p$characteristics_ch1 == "diagnosis: TCMR", 2, 3)))

gse48581_p$exact_diagnosis = ifelse(gse48581_p$characteristics_ch1.1 == "diagnosis (tcmr, abmr, mixed, non-rejecting, nephrectomy): non-rejecting", 0, ifelse(gse48581_p$characteristics_ch1.1 =="diagnosis (tcmr, abmr, mixed, non-rejecting, nephrectomy): ABMR", 1, ifelse(gse48581_p$characteristics_ch1.1 == "diagnosis (tcmr, abmr, mixed, non-rejecting, nephrectomy): TCMR", 2, 3)))

gse129166_p$exact_diagnosis = ifelse((gse129166_p$characteristics_ch1.1 == "tcmr (no: 0_borderline:1_TCMR:2): 0") & (gse129166_p$characteristics_ch1.2 == "abmr (no: 0_Yes:1): 0"), 0, ifelse((gse129166_p$characteristics_ch1.1 != "tcmr (no: 0_borderline:1_TCMR:2): 0") & (gse129166_p$characteristics_ch1.2 != "abmr (no: 0_Yes:1): 0"), 3, ifelse((gse129166_p$characteristics_ch1.1 != "tcmr (no: 0_borderline:1_TCMR:2): 0") & (gse129166_p$characteristics_ch1.2 == "abmr (no: 0_Yes:1): 0"), 2, 1)))

gse36059_p

gse48581_p

gse129166_p

Main outcomes are non-rejecting, TCMR (acute T-cell–mediated rejection), ABMR (anti-donor antibody-mediated rejection), and MIXED. Also has nephrectomy.

gse36059_ex = data.frame(t(exprs(gse36059)))
gse36059_ex

gse48581_ex = data.frame(t(exprs(gse48581)))
gse48581_ex

gse129166_ex = data.frame(t(exprs(gse129166)))
gse129166_ex

start = 1
stop = 100
boxplot(gse36059_ex[start:stop])

boxplot(gse48581_ex[start:stop])

boxplot(gse129166_ex[start:stop])